Cell Stress panel assay results from publication "Next Generation Risk Assessment for Occupational Chemical Safety – a Real World Example with Sodium-2-hydroxyethane sulfonate"
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ABSTRACT:
ORGANISM(S): Homo sapiens (human)
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PROVIDER: S-BSST1411 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description:A dose response and human cell line comparison of transcriptional responses following treatment with the chemical compound Sodium-2-hydroxyethane sulfonate. Gene expression changes were used to estimate the POD - minimum effect concentration when a biological perturbation as estimated by gene expression changes could be identified.
2024-12-31 | E-MTAB-14069 | biostudies-arrayexpress
Project description:Tempo-Seq experiment relating to Next Generation Risk Assessment for Occupational Chemical Safety – a Real World Example with Sodium-2-hydroxyethane sulfonate
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Project description:Several of the most important conservation prioritization approaches select markedly different areas at global and regional scales. They are designed to maximize a certain biodiversity dimension such as coverage of species in the case of hotspots and complementarity, or composite properties of ecosystems in the case of wilderness. Most comparisons between approaches have ignored the multidimensionality of biodiversity. We analyze here the results of two species-based methodologies-hotspots and complementarity-and an ecosystem-based methodology-wilderness-at local scale. As zoning of protected areas can increase the effectiveness of conservation, we use the data employed for the management plan of the Peneda-Gerês National Park in Portugal. We compare the approaches against four criteria: species representativeness, wilderness coverage, coverage of important areas for megafauna, and for regulating ecosystem services. Our results suggest that species- and ecosystem-based approaches select significantly different areas at local scale. Our results also show that no approach covers well all biodiversity dimensions. Species-based approaches cover species distribution better, while the ecosystem-based approach favors wilderness, areas important for megafauna, and for ecosystem services. Management actions addressing different dimensions of biodiversity have a potential for contradictory effects, social conflict, and ecosystem services trade-offs, especially in the context of current European biodiversity policies. However, biodiversity is multidimensional, and management and zoning at local level should reflect this aspect. The consideration of both species- and ecosystem-based approaches at local scale is necessary to achieve a wider range of conservation goals.
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Project description:The Patient-Centered Outcomes Research Institute has accelerated conversations about the importance of actively engaging stakeholders in all aspects of comparative effectiveness research (CER). Other scientific disciplines have a history of stakeholder engagement, yet few empirical examples exist of how these stakeholders can inform and enrich CER. Here we present a case study which includes the methods used to engage stakeholders, what we learned from them, and how we incorporated their ideas in a CER project. We selected stakeholders from key groups, built relationships with them and collected their feedback through interviews, observation and ongoing meetings during the four research process phases: proposal development, adapting study methods, understanding the context and information technology tool design and refinement.
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Project description:Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected ALK, RET, NTRK1, and ROS1 fusion isoforms and MET exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions.
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Project description:The organic anion of the title compound, {[Na(C(15)H(9)O(10)S)(H(2)O)(2)]·H(2)O}(n) {systematic name: poly[[diaqua-[?-2-(3,4-dihy-droxy-phen-yl)-3,5,7-trihy-droxy-4-oxo-4H-chromene-8-sulfon-ato]-sodium] monohydrate]}, has a nearly planar structure. The Na atom is six-coordinated by O atoms, two from water mol-ecules and four from the anion. The dihedral angle between the ring systems in the anion is 10.1?(1)°. Intra-molecular O-H?S and O-H?O inter-actions occur. In the crystal structure, an extensive network of classical inter-molecular O-H?S and O-H?O hydrogen bonds forms layers along the c axis.
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Project description:In the title compound, Na(+)·C(6)H(4)IO(3)S(-)·H(2)O, the Na atom is hexa-coordinated by O atoms, forming a two-dimensional sheet-like structure in the bc plane, with the iodo-benzene rings protruding above and below. Na⋯O contact distances are in the range 2.419 (2)-2.7218 (18) Å and O⋯Na⋯O angles are in the range 73.70 (5)-158.64 (7)°. The crystal structure is stabilized by O-H⋯O and C-H⋯O hydrogen bonds and C-H⋯π inter-actions. The I atom is disordered over two positions with occupancies of 0.78 (2) and 0.22 (2).
| S-EPMC2960107 | biostudies-literature
Project description:Carbon nanostructures (carbon nanotubes, nano carbon spheres, layered carbon nanostructures) were prepared from a sodium dodecyl sulfonate @ sodium chloride system. Sodium dodecyl sulfonate was used as a carbon source. A sodium chloride crystal in the carbonization procedure was used to separate ordered aggregates of sodium dodecyl sulfonate. The results show that different carbon nanostructures were prepared at low concentrations (1CMC~5CMC) by controlling the concentration of sodium dodecyl sulfonate, such as nano carbon spheres and carbon nanotubes, and that layered carbon nanostructures were formed at high concentrations (10CMC). The prepared carbon nanostructures were characterized by transmission electron microscopy, fluorescence spectrometry and Raman spectrometry. The results of this experiment show that the surfactant @ salt system is a potential method for the preparation of carbon nanostructures.
| S-EPMC9143293 | biostudies-literature
Project description:A new human coronavirus (CoV), subsequently named Middle East respiratory syndrome (MERS)-CoV, was first reported in Saudi Arabia in September 2012. In response, we developed two real-time reverse transcription-PCR (rRT-PCR) assays targeting the MERS-CoV nucleocapsid (N) gene and evaluated these assays as a panel with a previously published assay targeting the region upstream of the MERS-CoV envelope gene (upE) for the detection and confirmation of MERS-CoV infection. All assays detected ≤10 copies/reaction of quantified RNA transcripts, with a linear dynamic range of 8 log units and 1.3 × 10(-3) 50% tissue culture infective doses (TCID50)/ml of cultured MERS-CoV per reaction. All assays performed comparably with respiratory, serum, and stool specimens spiked with cultured virus. No false-positive amplifications were obtained with other human coronaviruses or common respiratory viral pathogens or with 336 diverse clinical specimens from non-MERS-CoV cases; specimens from two confirmed MERS-CoV cases were positive with all assay signatures. In June 2012, the U.S. Food and Drug Administration authorized emergency use of the rRT-PCR assay panel as an in vitro diagnostic test for MERS-CoV. A kit consisting of the three assay signatures and a positive control was assembled and distributed to public health laboratories in the United States and internationally to support MERS-CoV surveillance and public health responses.
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Project description:PurposeBreast cancer is one of the most common causes of cancer-related death in females. Numerous drug-targetable biomarkers and predictive biomarkers have been developed. Some researchers have expressed doubts about the need for next-generation sequencing (NGS) studies in daily practice. This study analyzed the results of NGS studies on breast cancer at a single institute and evaluated the real-world applications of NGS data to precision medicine for breast cancer.Materials and methodsWe retrospectively collected the results of NGS studies and analyzed the histopathologic features and genetic profiles of patients treated for breast cancer from 2010 to 2021. Seventy cases had data from CancerSCAN, a customized panel of 375 cancer-associated genes, and 110 cases had data from TruSight Oncology 500.ResultsThe most frequently detected single nucleotide variant was the TP53 mutation (123/180, 68.3%), followed by PIK3CA mutations (51/180, 28.3%). Estrogen receptor 1 (ESR1) mutation was detected in 11 patients (6.1%), of whom 10 had hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer, and two had no history of prior endocrine therapy. Based on their NGS study results, 13 patients (7.2%) received target therapy. Among them, four patients had a BRCA1 or BRCA2 germline mutation, and nine patients had a PIK3CA mutation.ConclusionNGS can provide information about predictive biomarkers and drug-targetable biomarkers that can enable treatment and participation in clinical trials based on precision medicine. Further studies should be conducted to excavate novel drug-targetable biomarkers and develop additional target therapies.
| S-EPMC10789952 | biostudies-literature